The MHC class II region is a principal susceptibility locus for multiple sclerosis (MS) and many other autoimmune diseases, indicating that peptide presentation to CD4 T cells is critical in the pathogenesis. The major goal of this project is develop novel strategies for the treatment of MS and other autoimmune diseases that target the MHC class II antigen presentation pathway. This program is a collaborative effort between the PI's lab and the Harvard Center for Neurodegeneration and Repair (HCNR) that has established a drug discovery program within our academic environment. During the previous funding period, we developed a novel real time peptide binding assay and identified several groups of small molecules that modulate peptide binding by MHC class II. The most interesting group of compounds is represented by a small molecule termed J10 that accelerates peptide loading more than 70-fold. This small molecule has functional similarities with HLA-DM, the protein that catalyzes loading of peptides onto MHC class II molecules in a late endosomal compartment. MHC class II-based therapeutics are inefficiently loaded onto MHC molecules because they are exposed to endosomal proteases for extended periods of time before they reach the HLA-DM compartment. J10 is active over a broad pH range, indicating that it may enable MHC class II binding of therapeutics in early endosomal compartments or at the cell surface. New data demonstrate that a J10 derivative is active in vivo and that it substantially enhances peptide display. Furthermore, covalent attachment of the J10 catalyst to the C-terminus of peptides substantially increases the efficiency of peptide loading both in vitro and in vivo. Our hypothesis is that the efficacy of MHC class II-based therapeutics can be substantially enhanced with a small molecule that catalyzes rapid binding to MHC class II molecules. The goals for the next funding period are to define their precise mechanisms of action and to test therapeutic applications in humanized mouse models of MS. In Aim 1, we will investigate the structural and functional mechanisms by which these small molecules accelerate peptide loading. We will map the J10 binding site by site-directed mutagenesis of candidate regions and co-crystallize J10 with DR/peptide complexes for structure determination by X-ray crystallography. In Aim 2, we will examine whether the therapeutic efficacy of three different classes of MHC class II-based therapeutics (Copaxone, tolerogenic self-peptides, MHC class II inhibitors) can be increased by co- administration or covalent attachment of J10. The medicinal chemistry component of this program will continue to synthesize derivatives with improved activity and drug-like properties for these. PUBLIC HEALTH RELEVANCE A number of therapeutic approaches for the treatment of autoimmune diseases require binding of the therapeutic to MHC class II molecules. A major issue is that loading of these compounds into the MHC class II binding site is inefficient because the natural catalyst that accelerates peptide loading is confined to a late endosomal compartment. We have discovered small molecules that substantially accelerate peptide binding to MHC class II molecules and will now examine their mechanism of action as well as therapeutic applications in humanized mouse models of MS.